branch-1-6/Bio/Expression/Platform.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Expression::Platform
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Allen Day <allenday@ucla.edu>
   8 #
   9 # Copyright Allen Day
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Expression::Platform - DESCRIPTION of Object
  18
  19 =head1 SYNOPSIS
  20
  21 Give standard usage here
  22
  23 =head1 DESCRIPTION
  24
  25 Describe the object here
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to
  33 the Bioperl mailing list.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 of the bugs and their resolution. Bug reports can be submitted via
  53 the web:
  54
  55   http://bugzilla.open-bio.org/
  56
  57 =head1 AUTHOR - Allen Day
  58
  59 Email allenday@ucla.edu
  60
  61 =head1 APPENDIX
  62
  63 The rest of the documentation details each of the object methods.
  64 Internal methods are usually preceded with a _
  65
  66 =cut
  67
  68
  69 # Let the code begin...
  70
  71
  72 package Bio::Expression::Platform;
  73 use strict;
  74 use base qw(Bio::Root::Root);
  75 use Bio::DB::Taxonomy;
  76
  77 =head2 new()
  78
  79  Usage   : my $obj = Bio::Expression::Platform->new();
  80  Function: Builds a new Bio::Expression::Platform object
  81  Returns : an instance of Bio::Expression::Platform
  82  Args    :
  83
  84 =cut
  85
  86 sub new {
  87   my($class,@args) = @_;
  88
  89   my $self = $class->SUPER::new(@args);
  90   $self->_initialize(@args);
  91   return $self;
  92 }
  93
  94 =head2 _initialize()
  95
  96  Usage   : $obj->_initialize(%arg);
  97  Function: Internal method to initialize a new Bio::Expression::Platform object
  98  Returns : true on success
  99  Args    : passed through to new()
 100
 101 =cut
 102
 103 sub _initialize {
 104   my($self,%arg) = @_;
 105
 106   foreach my $arg (keys %arg){
 107     my $marg = $arg;
 108     $marg =~ s/^-//;
 109     $self->$marg($arg{$arg}) if $self->can($marg);
 110   }
 111
 112   $self->taxdb( Bio::DB::Taxonomy->new(-source => 'entrez') );
 113   return 1;
 114 }
 115
 116
 117
 118 =head2 get_datasets()
 119
 120  Usage   :
 121  Function:
 122  Example :
 123  Returns :
 124  Args    :
 125
 126 =cut
 127
 128 sub get_datasets {
 129   my ($self,@args) = @_;
 130   my $db = $self->db();
 131
 132   my @datasets = $db->get_datasets( $self );
 133
 134   return @datasets;
 135 }
 136
 137 =head2 accession()
 138
 139  Usage   : $obj->accession($newval)
 140  Function:
 141  Example :
 142  Returns : value of accession (a scalar)
 143  Args    : on set, new value (a scalar or undef, optional)
 144
 145
 146 =cut
 147
 148 sub accession {
 149   my($self,$val) = @_;
 150   $self->{'accession'} = $val if defined($val);
 151   return $self->{'accession'};
 152 }
 153
 154 =head2 name()
 155
 156  Usage   : $obj->name($newval)
 157  Function:
 158  Example :
 159  Returns : value of name (a scalar)
 160  Args    : on set, new value (a scalar or undef, optional)
 161
 162
 163 =cut
 164
 165 sub name {
 166   my($self,$val) = @_;
 167   $self->{'name'} = $val if defined($val);
 168   return $self->{'name'};
 169 }
 170
 171 =head2 taxon()
 172
 173  Usage   : $obj->taxon()
 174  Function:
 175  Example :
 176  Returns : A Bio::Taxonomy::Node object
 177  Args    : none
 178
 179
 180 =cut
 181
 182 sub taxon {
 183   my($self) = @_;
 184   if ( ! $self->{'taxon'} ) {
 185     $self->{'taxon'} = $self->taxdb->get_Taxonomy_Node( $self->_taxon_id() );
 186   }
 187   return $self->{'taxon'};
 188 }
 189
 190 =head2 contact()
 191
 192  Usage   : $obj->contact($newval)
 193  Function:
 194  Example :
 195  Returns : a Bio::Expression::Contact object
 196  Args    : on set, new value (a scalar or undef, optional)
 197
 198
 199 =cut
 200
 201 sub contact {
 202   my($self,$val) = @_;
 203   $self->{'contact'} = $val if defined($val);
 204   return $self->{'contact'};
 205 }
 206
 207 =head2 db()
 208
 209  Usage   : $obj->db($newval)
 210  Function:
 211  Example :
 212  Returns : value of db (a scalar)
 213  Args    : on set, new value (a scalar or undef, optional)
 214
 215
 216 =cut
 217
 218 sub db {
 219   my($self,$val) = @_;
 220   $self->{'db'} = $val if defined($val);
 221   return $self->{'db'};
 222 }
 223
 224 =head2 _taxon_id()
 225
 226  Usage   : $obj->_taxon_id($newval)
 227  Function:
 228  Example :
 229  Returns : value of _taxon_id (a scalar)
 230  Args    : on set, new value (a scalar or undef, optional)
 231
 232
 233 =cut
 234
 235 sub _taxon_id {
 236   my($self,$val) = @_;
 237   $self->{'_taxon_id'} = $val if defined($val);
 238   return $self->{'_taxon_id'};
 239 }
 240
 241 =head2 taxdb()
 242
 243  Usage   : $obj->taxdb($newval)
 244  Function:
 245  Example :
 246  Returns : a Bio::DB::Taxonomy object
 247  Args    : on set, new value (a scalar or undef, optional)
 248
 249
 250 =cut
 251
 252 sub taxdb {
 253   my($self,$val) = @_;
 254   $self->{'taxdb'} = $val if defined($val);
 255   return $self->{'taxdb'};
 256 }
 257
 258
 259
 260 1;